GENEMARK PREDICTIONS Sequence: gi|85060411|ref|NC_007713.1| Sodalis glossinidius str. 'morsitans' plasmid pSG1, complete sequence Sequence file: NC_007713.fna Sequence length: 83306 GC Content: 48.88% Window length: 96 Window step: 12 Threshold value: 0.500 --- Matrix: - Matrix author: - Matrix order: 2 List of Open reading frames predicted as CDSs, shown with alternate starts (regions from start to stop codon w/ coding function >0.50) Left Right DNA Coding Avg Start end end Strand Frame Prob Prob -------- -------- ---------- ----- ---- ---- 673 948 direct fr 1 0.81 0.85 718 948 direct fr 1 0.79 0.07 994 1950 direct fr 1 0.85 0.93 1000 1950 direct fr 1 0.86 0.67 1093 1950 direct fr 1 0.87 0.84 1162 1950 direct fr 1 0.88 0.14 1348 1950 direct fr 1 0.89 0.30 2345 2494 direct fr 2 0.61 0.81 2354 2494 direct fr 2 0.61 0.09 2509 2943 direct fr 1 0.77 0.62 2611 2943 direct fr 1 0.82 0.33 2632 2943 direct fr 1 0.80 0.40 8407 8637 direct fr 1 0.55 0.02 8512 8637 direct fr 1 0.64 0.17 8515 8637 direct fr 1 0.64 0.26 9165 9665 direct fr 3 0.56 0.20 9210 9665 direct fr 3 0.55 0.51 10472 10762 direct fr 2 0.52 0.78 11126 11464 direct fr 2 0.66 0.99 11174 11464 direct fr 2 0.62 0.00 11213 11464 direct fr 2 0.56 0.03 11642 11857 direct fr 2 0.55 0.58 12228 12455 direct fr 3 0.73 0.67 12234 12455 direct fr 3 0.75 0.29 14918 15109 direct fr 2 0.57 0.98 14954 15109 direct fr 2 0.52 0.24 15830 15997 direct fr 2 0.65 0.99 15863 15997 direct fr 2 0.73 0.44 15866 15997 direct fr 2 0.79 0.16 15899 15997 direct fr 2 0.75 0.03 15902 15997 direct fr 2 0.72 0.01 16374 16952 direct fr 3 0.51 1.00 17082 18542 direct fr 3 0.64 0.50 17226 18542 direct fr 3 0.61 0.23 17352 18542 direct fr 3 0.58 0.61 18600 18743 direct fr 3 0.70 0.13 18627 18743 direct fr 3 0.61 0.18 19217 19489 direct fr 2 0.52 0.84 20742 20834 direct fr 3 0.71 0.84 21147 21401 direct fr 3 0.53 0.05 21150 21401 direct fr 3 0.53 0.09 21720 21848 complement fr 2 0.62 0.86 21720 21824 complement fr 2 0.55 0.78 21944 22141 direct fr 2 0.95 0.99 21974 22141 direct fr 2 0.98 0.03 22148 22579 direct fr 2 0.77 0.46 22196 22579 direct fr 2 0.75 0.04 22259 22579 direct fr 2 0.70 0.02 22576 22725 direct fr 1 0.51 0.80 22744 23949 direct fr 1 0.83 0.97 22756 23949 direct fr 1 0.83 0.68 22834 23949 direct fr 1 0.85 0.05 22885 23949 direct fr 1 0.85 0.20 22894 23949 direct fr 1 0.85 0.19 22915 23949 direct fr 1 0.85 0.01 22963 23949 direct fr 1 0.86 0.09 23374 23949 direct fr 1 0.84 0.09 23946 24893 direct fr 3 0.91 0.44 23973 24893 direct fr 3 0.93 0.32 24117 24893 direct fr 3 0.93 0.02 24132 24893 direct fr 3 0.93 0.01 24219 24893 direct fr 3 0.92 0.13 24961 25425 direct fr 1 0.59 0.80 25057 25425 direct fr 1 0.63 0.04 25105 25425 direct fr 1 0.68 0.46 25162 25425 direct fr 1 0.68 0.63 25195 25425 direct fr 1 0.64 0.35 25198 25425 direct fr 1 0.64 0.14 29795 29911 direct fr 2 0.54 0.47 29831 30739 complement fr 1 0.88 0.19 29831 30727 complement fr 1 0.90 0.07 29831 30679 complement fr 1 0.93 0.26 29831 30604 complement fr 1 0.93 0.38 29831 30526 complement fr 1 0.92 0.19 30720 31049 complement fr 2 0.57 0.54 30720 31040 complement fr 2 0.55 0.81 30720 31019 complement fr 2 0.52 0.96 31149 31667 complement fr 2 0.81 0.82 31149 31640 complement fr 2 0.80 0.48 31149 31610 complement fr 2 0.79 0.12 31671 32036 complement fr 2 0.99 0.78 31671 32030 complement fr 2 0.99 0.27 31671 32012 complement fr 2 0.99 0.02 32027 32203 complement fr 1 0.92 0.19 32027 32194 complement fr 1 0.91 0.05 32027 32152 complement fr 1 0.89 0.01 32258 32662 complement fr 1 0.86 0.14 32258 32611 complement fr 1 0.84 0.10 32258 32590 complement fr 1 0.82 0.11 32742 32975 complement fr 2 0.78 0.19 32742 32891 complement fr 2 0.69 0.43 32742 32879 complement fr 2 0.67 0.52 33228 33782 complement fr 2 0.86 0.03 33228 33764 complement fr 2 0.87 0.03 33228 33677 complement fr 2 0.92 0.78 33228 33653 complement fr 2 0.91 0.36 33749 33877 complement fr 1 0.51 0.41 33939 34160 complement fr 2 0.79 0.95 33939 34091 complement fr 2 0.70 0.04 33939 34028 complement fr 2 0.51 0.00 34106 34357 complement fr 1 0.73 0.38 34106 34342 complement fr 1 0.70 0.01 34106 34306 complement fr 1 0.65 0.04 34273 34521 complement fr 3 0.51 0.87 34537 34743 complement fr 3 0.99 0.83 34537 34740 complement fr 3 0.99 0.72 34537 34671 complement fr 3 0.98 0.02 34731 34862 complement fr 2 0.64 0.00 34731 34841 complement fr 2 0.57 0.01 35099 35194 complement fr 1 0.87 0.10 35099 35179 complement fr 1 0.87 0.15 35191 35343 complement fr 3 0.76 0.15 35191 35310 complement fr 3 0.70 0.08 35191 35280 complement fr 3 0.59 0.23 35280 36095 complement fr 2 0.79 0.86 35280 36080 complement fr 2 0.79 0.86 35280 36041 complement fr 2 0.78 0.02 36227 36442 complement fr 1 0.83 0.06 36227 36439 complement fr 1 0.83 0.02 36227 36370 complement fr 1 0.99 0.99 36227 36358 complement fr 1 0.99 0.52 36227 36313 complement fr 1 0.98 0.00 36238 36645 complement fr 3 0.57 0.92 36688 36732 complement fr 3 0.57 0.00 36801 37010 complement fr 2 0.86 0.89 36801 36965 complement fr 2 1.00 0.21 36801 36959 complement fr 2 1.00 0.05 36801 36926 complement fr 2 1.00 0.02 37007 37630 complement fr 1 0.93 0.01 37007 37618 complement fr 1 0.95 0.32 37007 37588 complement fr 1 0.97 1.00 37007 37564 complement fr 1 0.97 0.41 37007 37357 complement fr 1 0.96 0.36 37716 38672 complement fr 2 0.84 0.50 37716 38576 complement fr 2 0.86 0.00 37716 38489 complement fr 2 0.91 0.88 37716 38486 complement fr 2 0.91 0.91 38365 39126 complement fr 3 0.55 0.97 38365 39078 complement fr 3 0.55 0.03 38365 39048 complement fr 3 0.53 0.00 38365 39039 complement fr 3 0.53 0.00 39274 39687 complement fr 3 0.60 0.29 39274 39609 complement fr 3 0.64 0.02 39274 39465 complement fr 3 0.63 0.02 39274 39453 complement fr 3 0.61 0.04 39665 40009 complement fr 1 0.81 0.62 39665 39997 complement fr 1 0.83 0.71 39665 39970 complement fr 1 0.86 0.83 39665 39961 complement fr 1 0.86 0.35 39665 39943 complement fr 1 0.85 0.26 39958 40308 complement fr 3 0.86 0.04 39958 40179 complement fr 3 0.79 0.12 39958 40125 complement fr 3 0.71 0.14 40308 40577 complement fr 2 0.65 0.75 40308 40574 complement fr 2 0.65 0.62 40308 40541 complement fr 2 0.60 0.03 40574 40900 complement fr 1 0.58 0.00 40574 40792 complement fr 1 0.72 0.40 40574 40774 complement fr 1 0.68 0.00 40574 40753 complement fr 1 0.66 0.00 40815 40859 complement fr 2 0.52 0.00 40914 41294 complement fr 2 0.53 0.00 40914 41234 complement fr 2 0.63 0.09 40914 41192 complement fr 2 0.73 0.00 40914 41117 complement fr 2 0.91 0.37 40914 41096 complement fr 2 0.90 0.00 40914 41045 complement fr 2 0.88 0.43 41192 41812 complement fr 1 0.93 0.97 41192 41809 complement fr 1 0.93 0.93 41192 41776 complement fr 1 0.93 0.03 41799 41969 complement fr 2 0.59 0.00 41799 41936 complement fr 2 0.51 0.80 42131 42487 complement fr 1 0.76 0.12 42131 42436 complement fr 1 0.84 0.62 42131 42406 complement fr 1 0.82 0.11 42131 42349 complement fr 1 0.78 0.05 42815 43012 complement fr 1 0.69 0.80 42815 42994 complement fr 1 0.77 0.14 42815 42925 complement fr 1 0.83 0.81 42815 42913 complement fr 1 0.81 0.64 42815 42910 complement fr 1 0.79 0.27 46021 46455 complement fr 3 0.66 0.73 46021 46437 complement fr 3 0.64 0.71 46021 46140 complement fr 3 0.57 0.22 46959 47402 complement fr 2 0.85 0.52 46959 47396 complement fr 2 0.87 0.69 46959 47327 complement fr 2 0.88 0.01 46959 47276 complement fr 2 0.86 0.22 46959 47261 complement fr 2 0.85 0.02 47493 47672 direct fr 3 0.58 0.92 47508 47672 direct fr 3 0.58 0.42 47517 47882 complement fr 2 0.65 0.13 47517 47786 complement fr 2 0.67 0.29 47517 47696 complement fr 2 0.51 0.36 47517 47693 complement fr 2 0.51 0.34 53722 54699 complement fr 3 0.86 0.03 53722 54648 complement fr 3 0.91 0.75 53722 54612 complement fr 3 0.91 0.18 53722 54480 complement fr 3 0.90 0.03 53722 54447 complement fr 3 0.90 0.09 54645 55136 complement fr 2 0.78 0.16 54645 55082 complement fr 2 0.82 0.34 54645 54890 complement fr 2 0.77 0.00 54645 54839 complement fr 2 0.71 0.80 55387 56112 complement fr 3 0.61 0.00 55387 56031 complement fr 3 0.68 0.00 55387 55974 complement fr 3 0.74 0.95 55387 55941 complement fr 3 0.77 0.01 55387 55911 complement fr 3 0.78 0.06 55387 55899 complement fr 3 0.80 0.64 55387 55827 complement fr 3 0.78 0.42 55853 56137 complement fr 1 0.69 0.52 55853 56044 complement fr 1 0.60 0.16 55853 56008 complement fr 1 0.51 0.00 56109 56408 complement fr 2 0.52 0.70 56109 56387 complement fr 2 0.50 0.94 56549 56677 direct fr 2 0.64 0.07 57007 57231 complement fr 3 0.50 0.34 57423 57587 complement fr 2 0.50 0.68 57423 57578 complement fr 2 0.50 0.98 57659 58294 complement fr 1 0.88 0.85 57659 58285 complement fr 1 0.88 0.30 57659 58279 complement fr 1 0.88 0.51 58291 59145 complement fr 3 0.75 0.00 58291 59088 complement fr 3 0.81 0.45 58291 59061 complement fr 3 0.83 0.82 58291 58863 complement fr 3 0.84 0.73 58291 58827 complement fr 3 0.84 0.33 58291 58740 complement fr 3 0.80 0.18 59058 59846 complement fr 2 0.89 0.67 59058 59843 complement fr 2 0.91 0.66 59058 59750 complement fr 2 0.91 0.03 59058 59624 complement fr 2 0.89 0.12 59058 59594 complement fr 2 0.89 0.01 59860 60903 complement fr 3 0.89 0.68 59860 60891 complement fr 3 0.90 0.55 59860 60840 complement fr 3 0.89 0.74 59860 60822 complement fr 3 0.89 0.39 60884 61870 complement fr 1 0.94 0.99 60884 61858 complement fr 1 0.95 0.99 60884 61831 complement fr 1 0.95 0.03 60884 61819 complement fr 1 0.95 0.02 61867 62847 complement fr 3 0.87 0.00 61867 62784 complement fr 3 0.93 0.57 61867 62709 complement fr 3 0.93 0.61 61867 62670 complement fr 3 0.93 0.12 62774 64630 complement fr 1 0.94 0.91 62774 64621 complement fr 1 0.94 0.85 62774 64591 complement fr 1 0.94 0.31 64623 65399 complement fr 2 0.84 0.98 64623 65318 complement fr 2 0.83 0.13 64623 65279 complement fr 2 0.81 0.00 65393 67213 complement fr 1 0.91 0.88 65393 67132 complement fr 1 0.93 0.03 65393 67129 complement fr 1 0.93 0.02 65393 67093 complement fr 1 0.92 0.01 67227 68663 complement fr 2 0.87 0.01 67227 68648 complement fr 2 0.88 0.03 67227 68615 complement fr 2 0.90 0.77 67227 68594 complement fr 2 0.91 0.85 67227 68492 complement fr 2 0.91 0.00 67227 68462 complement fr 2 0.91 0.09 68606 69811 complement fr 1 0.82 1.00 68606 69790 complement fr 1 0.82 0.99 68606 69787 complement fr 1 0.82 0.97 69804 71588 complement fr 2 0.96 0.96 69804 71456 complement fr 2 0.98 0.13 69804 71405 complement fr 2 0.98 0.42 69804 71357 complement fr 2 0.98 0.45 71626 73731 complement fr 3 0.93 0.27 71626 73704 complement fr 3 0.94 1.00 71626 73641 complement fr 3 0.94 0.00 71626 73638 complement fr 3 0.94 0.00 73835 75211 complement fr 1 0.90 0.25 73835 75058 complement fr 1 0.93 0.15 73835 74944 complement fr 1 0.93 0.10 73835 74791 complement fr 1 0.93 0.05 75641 75976 direct fr 2 0.76 0.69 75653 75976 direct fr 2 0.78 0.55 75707 75976 direct fr 2 0.83 0.17 75830 75976 direct fr 2 0.70 0.05 75988 76089 direct fr 1 0.70 0.99 75997 76089 direct fr 1 0.67 0.40 76174 76653 direct fr 1 0.81 0.06 76243 76653 direct fr 1 0.82 0.70 76252 76653 direct fr 1 0.84 0.23 76285 76653 direct fr 1 0.85 0.52 76663 76869 direct fr 1 0.76 0.30 76699 76869 direct fr 1 0.71 0.57 76735 76869 direct fr 1 0.64 0.66 77329 77673 direct fr 1 0.79 0.14 77509 77673 direct fr 1 0.87 0.82 77834 78412 direct fr 2 0.76 0.03 77993 78412 direct fr 2 0.78 0.30 78014 78412 direct fr 2 0.77 0.14 78017 78412 direct fr 2 0.77 0.06 78580 78699 direct fr 1 0.64 0.32 79259 79750 complement fr 1 0.84 0.24 79259 79726 complement fr 1 0.88 0.71 79259 79681 complement fr 1 0.88 0.42 79259 79579 complement fr 1 0.83 0.00 79850 80665 direct fr 2 0.59 0.05 79964 80665 direct fr 2 0.62 0.54 80018 80665 direct fr 2 0.59 0.05 80066 80665 direct fr 2 0.56 0.76 80461 80931 direct fr 1 0.68 0.10 80491 80931 direct fr 1 0.66 0.42 80689 80931 direct fr 1 0.50 0.34 80707 80931 direct fr 1 0.52 0.05 81072 81335 direct fr 3 0.67 0.04 81108 81335 direct fr 3 0.68 0.05 81135 81335 direct fr 3 0.71 0.90 81710 82003 direct fr 2 0.54 0.14 81728 82003 direct fr 2 0.57 0.22 81809 82003 direct fr 2 0.60 0.71 81818 82003 direct fr 2 0.57 0.25 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 619 948 direct fr 1 846 1022 direct fr 3 946 1950 direct fr 1 967 1404 complement fr 3 1863 2231 direct fr 3 2276 2494 direct fr 2 2488 2943 direct fr 1 6407 6589 complement fr 1 7160 7318 complement fr 1 8158 8637 direct fr 1 8973 9665 direct fr 3 10262 10762 direct fr 2 11120 11464 direct fr 2 11462 11857 direct fr 2 11839 12237 direct fr 1 12174 12455 direct fr 3 12453 12971 direct fr 3 13265 13930 direct fr 2 14609 15109 direct fr 2 15173 15703 direct fr 2 15806 15997 direct fr 2 16000 16377 direct fr 1 16290 16952 direct fr 3 17001 18542 direct fr 3 18540 18743 direct fr 3 18808 19182 direct fr 1 19064 19489 direct fr 2 20075 20932 direct fr 2 20670 20834 direct fr 3 21045 21401 direct fr 3 21475 22053 complement fr 3 21720 21938 complement fr 2 21896 22141 direct fr 2 21905 22729 complement fr 1 22139 22579 direct fr 2 22513 22725 direct fr 1 22723 23949 direct fr 1 23922 24893 direct fr 3 24946 25353 complement fr 3 24955 25425 direct fr 1 27931 28440 direct fr 1 28797 28997 direct fr 3 28968 29219 complement fr 2 29590 29859 direct fr 1 29759 29911 direct fr 2 29831 30742 complement fr 1 30720 31151 complement fr 2 31002 31514 direct fr 3 31149 31673 complement fr 2 31671 32066 complement fr 2 32027 32260 complement fr 1 32258 32758 complement fr 1 32742 33047 complement fr 2 32876 33205 complement fr 1 32942 33580 direct fr 2 33228 33854 complement fr 2 33749 33991 complement fr 1 33939 34280 complement fr 2 34106 34426 complement fr 1 34273 34539 complement fr 3 34537 34941 complement fr 3 34731 35081 complement fr 2 34802 35101 complement fr 1 35099 35257 complement fr 1 35191 35514 complement fr 3 35280 36266 complement fr 2 35945 36484 direct fr 2 36227 36481 complement fr 1 36238 36690 complement fr 3 36801 37028 complement fr 2 37007 37645 complement fr 1 37627 37833 complement fr 3 37716 38684 complement fr 2 38365 39153 complement fr 3 38906 39370 complement fr 1 39274 39771 complement fr 3 39462 39686 complement fr 2 39665 40057 complement fr 1 39958 40446 complement fr 3 40308 40655 complement fr 2 40574 40921 complement fr 1 40815 40916 complement fr 2 40914 41315 complement fr 2 40969 41229 complement fr 3 41192 41848 complement fr 1 41799 42503 complement fr 2 42131 42499 complement fr 1 42497 42817 complement fr 1 42815 43084 complement fr 1 43235 43513 complement fr 1 46021 46542 complement fr 3 46534 46713 direct fr 1 46640 46882 direct fr 2 46711 46905 direct fr 1 46959 47420 complement fr 2 47361 47672 direct fr 3 47517 47903 complement fr 2 48537 48947 direct fr 3 49337 49480 direct fr 2 49540 49896 complement fr 3 49612 50169 direct fr 1 49865 50062 direct fr 2 53722 54798 complement fr 3 54645 55166 complement fr 2 55084 55608 direct fr 1 55387 56121 complement fr 3 55853 56209 complement fr 1 56091 56297 direct fr 3 56109 56468 complement fr 2 56243 56677 direct fr 2 56392 56748 complement fr 3 56773 56967 complement fr 3 56806 57039 direct fr 1 57007 57279 complement fr 3 57170 57391 complement fr 1 57423 57776 complement fr 2 57659 58339 complement fr 1 58291 59160 complement fr 3 59058 59879 complement fr 2 59860 60948 complement fr 3 60884 61900 complement fr 1 61867 62862 complement fr 3 62774 64714 complement fr 1 64410 64886 direct fr 3 64623 65441 complement fr 2 65393 67225 complement fr 1 67227 68672 complement fr 2 68606 69817 complement fr 1 68633 69007 direct fr 2 69804 71591 complement fr 2 71626 73737 complement fr 3 73835 75226 complement fr 1 75343 75609 complement fr 3 75617 75976 direct fr 2 75892 76089 direct fr 1 76087 76653 direct fr 1 76651 76869 direct fr 1 77269 77673 direct fr 1 77777 78412 direct fr 2 78300 78518 direct fr 3 78373 78699 direct fr 1 79259 79774 complement fr 1 79811 80665 direct fr 2 80311 80931 direct fr 1 80844 81335 direct fr 3 81362 81583 complement fr 1 81683 82003 direct fr 2 POSSIBLE SEQUENCE FRAMESHIFTS DETECTED From To Frame Frame At base... ----- ----- ---------- 2 3 20748 +/- 11 bp (direct) 1 3 25344 +/- 11 bp (direct) 1 2 32988 +/- 11 bp (complement) 1 2 33804 +/- 11 bp (complement) 1 2 34164 +/- 11 bp (complement) 3 1 34368 +/- 11 bp (complement) 1 2 34908 +/- 11 bp (complement) 2 3 35436 +/- 11 bp (complement) 3 1 36396 +/- 11 bp (complement) 3 2 38676 +/- 11 bp (complement) 1 3 39096 +/- 11 bp (complement) 3 1 39324 +/- 11 bp (complement) 2 3 40392 +/- 11 bp (complement) 1 2 49920 +/- 11 bp (direct) 2 1 80400 +/- 11 bp (direct) 1 3 80856 +/- 11 bp (direct) -------------------- ABOUT THE MATRIX USED: Training set derived by GeneMarkS, 4.6a Fri Apr 20 20:47:35 2007